-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_4010668-4197625

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_13-snap.795-T1
Valid prediction for GlimmerHMM_glimmerT_31482-T1
Valid prediction for snap_scaffold_13-snap.747-T1
Valid prediction for Augustus_model.g20926.t1
Valid prediction for GlimmerHMM_glimmerT_31471-T1
Valid prediction for GlimmerHMM_glimmerT_31479-T1
Valid prediction for snap_scaffold_13-snap.771-T1
Valid prediction for snap_scaffold_13-snap.757-T1
Valid prediction for HiQ_model.g20932.t1
Valid prediction for snap_scaffold_13-snap.786-T1
Valid prediction for snap_scaffold_13-snap.774-T1
Valid prediction for snap_scaffold_13-snap.746-T1
Valid prediction for snap_scaffold_13-snap.770-T1
Valid prediction for Augustus_model.g20938.t1
Couldn't classify 64577, 64684
Sorry, prediction pasa_asmbl_10755.p1 fails validation.
(GGT)	 CA	64577-64684	GT	AGG
(ATC)	 AG	64896-64995	GT	GTG
(GCT)	 AG	65217-65392	GT	TGG
(ACT)	 AG	65711-65840	GT	TGG
(CCT)	 AG	66232-66341	AT	AGA
-recovered pasa_asmbl_10755.p1, terminal, 66232, 66341
-recovered pasa_asmbl_10755.p1, internal, 64896, 64995
-recovered pasa_asmbl_10755.p1, internal, 65217, 65392
-recovered pasa_asmbl_10755.p1, internal, 65711, 65840
Valid prediction for GlimmerHMM_glimmerT_31491-T1
Valid prediction for GlimmerHMM_glimmerT_31485-T1
Valid prediction for snap_scaffold_13-snap.775-T1
Valid prediction for snap_scaffold_13-snap.751-T1
Valid prediction for Augustus_model.g20945.t1
Valid prediction for snap_scaffold_13-snap.755-T1
Valid prediction for GlimmerHMM_glimmerT_31484-T1
Couldn't classify 2775, 3056
Sorry, prediction pasa_asmbl_10751.p1 fails validation.
(ATG)	 AA	2775-3056	GA	GCG
Valid prediction for snap_scaffold_13-snap.748-T1
Valid prediction for snap_scaffold_13-snap.790-T1
Valid prediction for GlimmerHMM_glimmerT_31464-T1
Valid prediction for snap_scaffold_13-snap.777-T1
Valid prediction for snap_scaffold_13-snap.764-T1
Valid prediction for GlimmerHMM_glimmerT_31470-T1
Valid prediction for GlimmerHMM_glimmerT_31480-T1
Valid prediction for Augustus_model.g20944.t1
Valid prediction for pasa_asmbl_10761.p1
Valid prediction for GlimmerHMM_glimmerT_31477-T1
Valid prediction for Augustus_model.g20929.t1
Valid prediction for snap_scaffold_13-snap.778-T1
Valid prediction for pasa_asmbl_10759.p1
Valid prediction for snap_scaffold_13-snap.752-T1
Valid prediction for snap_scaffold_13-snap.753-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.785-T1
Valid prediction for snap_scaffold_13-snap.793-T1
Valid prediction for GlimmerHMM_glimmerT_31473-T1
Valid prediction for Augustus_model.g20930.t1
Valid prediction for Augustus_model.g20937.t1
Valid prediction for Augustus_model.g20940.t1
Valid prediction for GlimmerHMM_glimmerT_31465-T1
Valid prediction for pasa_asmbl_10753.p1
Valid prediction for GlimmerHMM_glimmerT_31472-T1
Valid prediction for Augustus_model.g20936.t1
Valid prediction for GlimmerHMM_glimmerT_31492-T1
Valid prediction for CodingQuarry_transcript_12981-T1
Valid prediction for Augustus_model.g20946.t1
Valid prediction for snap_scaffold_13-snap.784-T1
Valid prediction for HiQ_model.g20933.t1
Valid prediction for GlimmerHMM_glimmerT_31489-T1
Valid prediction for snap_scaffold_13-snap.766-T1
Couldn't classify 182490, 182642
Couldn't classify 185363, 185374
Sorry, prediction pasa_asmbl_10765.p1 fails validation.
(TCT)	 GC	182490-182642	GT	AGG
(GAC)	 AG	184352-184468	GT	AGG
(ATG)	 AG	184883-185101	GT	AGG
(ATT)	 AG	185363-185374	AG	AGA
-recovered pasa_asmbl_10765.p1, initial, 184883, 185101
-recovered pasa_asmbl_10765.p1, internal, 184352, 184468
-recovered pasa_asmbl_10765.p1, internal, 184883, 185101
Valid prediction for snap_scaffold_13-snap.769-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31487-T1
Valid prediction for snap_scaffold_13-snap.787-T1
Valid prediction for GlimmerHMM_glimmerT_31476-T1
Valid prediction for snap_scaffold_13-snap.763-T1
Valid prediction for Augustus_model.g20947.t1
Valid prediction for snap_scaffold_13-snap.760-T1
Valid prediction for snap_scaffold_13-snap.761-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.772-T1
Valid prediction for snap_scaffold_13-snap.765-T1
Valid prediction for HiQ_model.g20931.t1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_13-snap.767-T1
Valid prediction for Augustus_model.g20942.t1
Valid prediction for snap_scaffold_13-snap.773-T1
Valid prediction for GlimmerHMM_glimmerT_31483-T1
Valid prediction for snap_scaffold_13-snap.794-T1
Valid prediction for snap_scaffold_13-snap.781-T1
Valid prediction for snap_scaffold_13-snap.780-T1
Valid prediction for snap_scaffold_13-snap.789-T1
Valid prediction for Augustus_model.g20928.t1
Valid prediction for Augustus_model.g20934.t1
Valid prediction for snap_scaffold_13-snap.776-T1
Valid prediction for snap_scaffold_13-snap.756-T1
Valid prediction for snap_scaffold_13-snap.791-T1
Valid prediction for Augustus_model.g20935.t1
Valid prediction for HiQ_model.g20943.t1
Valid prediction for GlimmerHMM_glimmerT_31481-T1
Valid prediction for GlimmerHMM_glimmerT_31467-T1
Valid prediction for GlimmerHMM_glimmerT_31469-T1
Valid prediction for snap_scaffold_13-snap.779-T1
Valid prediction for Augustus_model.g20941.t1
Valid prediction for Augustus_model.g20939.t1
Valid prediction for GlimmerHMM_glimmerT_31466-T1
Valid prediction for GlimmerHMM_glimmerT_31488-T1
Valid prediction for GlimmerHMM_glimmerT_31475-T1
Valid prediction for snap_scaffold_13-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_31486-T1
Valid prediction for GlimmerHMM_glimmerT_31478-T1
Valid prediction for snap_scaffold_13-snap.754-T1
Valid prediction for GlimmerHMM_glimmerT_31468-T1
Valid prediction for snap_scaffold_13-snap.749-T1
Valid prediction for snap_scaffold_13-snap.783-T1
Valid prediction for snap_scaffold_13-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_31490-T1
Valid prediction for snap_scaffold_13-snap.762-T1
Valid prediction for snap_scaffold_13-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_31474-T1
Couldn't classify 36219, 36320
Couldn't classify 41841, 42020
Sorry, prediction pasa_asmbl_9605.p1 fails validation.
(CAG)	 GA	36219-36320	GT	AGG
(GCC)	 AG	36845-36898	GT	TGG
(GTT)	 AG	37063-37154	GT	AGG
(TCA)	 AG	37305-37440	GT	AGG
(GTC)	 AG	37961-38072	GT	CGG
(GTC)	 AG	38162-38258	GT	AGG
(GTA)	 AG	39541-39658	GT	CTG
(CAC)	 AG	39949-40059	GT	TGG
(TTC)	 AG	41841-42020	TA	AGT
-recovered pasa_asmbl_9605.p1, internal, 36845, 36898
-recovered pasa_asmbl_9605.p1, internal, 37063, 37154
-recovered pasa_asmbl_9605.p1, internal, 37305, 37440
-recovered pasa_asmbl_9605.p1, internal, 37961, 38072
-recovered pasa_asmbl_9605.p1, internal, 38162, 38258
-recovered pasa_asmbl_9605.p1, internal, 39541, 39658
-recovered pasa_asmbl_9605.p1, internal, 39949, 40059
Valid prediction for snap_scaffold_13-snap.768-T1
Valid prediction for snap_scaffold_13-snap.759-T1
Valid prediction for Augustus_model.g20927.t1
Valid prediction for snap_scaffold_13-snap.792-T1
Valid prediction for snap_scaffold_13-snap.750-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21210, rend_intergenic: 10571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25726, rend_intergenic: 22038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26908, rend_intergenic: 26035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31815, rend_intergenic: 29239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33200, rend_intergenic: 32467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34988, rend_intergenic: 33234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106010, rend_intergenic: 102973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177844, rend_intergenic: 175331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179926, rend_intergenic: 179331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185157, rend_intergenic: 181609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186958
-exon list size: 380


building trellis

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17.8    
18.1    
18.3    
18.6    
18.8    
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20.7    
20.9    
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23.6    
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25.4    
25.7    
25.9    
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26.4    
26.7    
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27.7    
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28.3    
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29.6    
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31.9    
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32.7    
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33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.9    
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36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
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38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.7    
42.9    
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43.5    
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44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.1    
47.4    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
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51.3    
51.6    
51.8    
52.1    
52.4    
52.6    
52.9    
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53.4    
53.7    
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54.7    
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55.2    
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55.8    
56.0    
56.3    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.1    
58.4    
58.6    
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59.4    
59.7    
59.9    
60.2    
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63.4    
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64.4    
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65.2    
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68.1    
68.3    
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70.2    
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73.0    
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73.6    
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74.1    
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74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
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78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
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80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
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82.5    
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83.0    
83.2    
83.5    
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84.0    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 21210, rend_intergenic: 10571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25726, rend_intergenic: 22038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26908, rend_intergenic: 26035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31815, rend_intergenic: 29239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33200, rend_intergenic: 32467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34988, rend_intergenic: 33234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106010, rend_intergenic: 102973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177844, rend_intergenic: 175331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179926, rend_intergenic: 179331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185157, rend_intergenic: 181609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support